I have found some promising (old) articles but the trail has run cold.
Ideally I am looking for working plugins/code, but if they are simply not available, then any concrete directions on how to build probabilistic and/or defeasible reasoning for integration into Protege would still be useful.
RaMP Defeasible Reasoning plugin for Protege. Appears to be dormant/abandoned. Perhaps project/code was lost along with http://code.google.com/p/nomor/
PR-OWL http://www.pr-owl.org/. Extends OWL to support probabilistic ontologies. Appears to be dormant/abandoned.
Defeasible RuleML looked interesting, but I cannot find any concrete implementations/plugins/code. http://ruleml.org/1.0/defeasible/defeasible.html.
Defeasible Logic RuleML-compatible Rule
Language. Even if code can be found, this implementation looks experimental, and does not leverage more recent standards and formats. Paper: http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.103.5914&rep=rep1&type=pdf Resources: http://lpis.csd.auth.gr/systems/resources.html#drdchairruleml2010
There's Pronto (available here), which is built on top of Pellet. I cannot recall if it comes as a Protege plugin, but as it is tied to Pellet I imagine it shouldn't be too hard to implement an OWLReasoner wrapper for the two.
Related
I'm new in "ontology world". I've been practicing Protegé and ontologies for 2 months and now I would like to understand (and if it is possible to create) a reasoner. But I don't know what is its structure, the language used by it and so on.
Can you please me provide me a piece of information and something to read? Thank you.
The task of a reasoner is to produce inferences. Standard reasoning tasks are consistency check, realization, instance check and satisfiability. You can find all these defined in a number of books and articles about description logic.
Protege uses the OWL API to interface to reasoners so they are implementations of OWLReasoner. Not all of them are written in Java (e.g., FaCT++ is written in C++).
They are quite complex systems, so describing how to implement one takes chapters - too big for an answer here.
I'd recommend exploring the source code of a few of them. Open Source ones, off the top of my head: HermiT, FaCT++, Pellet, JFact, ELK.
I'm working on an OWL ontology and I need some specific issues
I only need ontology schema (TBox) and I got lost, what are the operations that can be
completed using reasoning and sparql and OWL API?
More specifically, I need the following:
1- check cardinalities between classes and properties.
2- find subsumption relationships for a specific class.
3- check whether specific facts hold (e.g. are two classes are disjoint)
4- find the paths (a class-property series) between a set of classes.
What each of reasoning, sparql and OWL API used for? and which one is suitable for my situation?
Actually I don't know how to start and what technique to use.
In addition. Would you please refer me to some reference?
Thanks.
Number 1 is not clear: do you want to know which cardinality axioms are asserted? This can be done without a reasoner. Number 4 is a bit vague as well, can you provide an example?
2, 3 and 5 require a reasoner to be perform accurately.
A reasoner is a program that will explicit implicit information: subsumption, realisation, consistency checks are all operations for which a reasoner is needed. In your tasks, subsumption is clearly needed.
OWLAPI is a Java API to manipulate OWL ontologies; in your case, it could be useful to write the connecting code to use a reasoner for your tasks. Compatible reasoners are Pellet, HermiT, FaCT++, and a few more.
SPARQL is an RDF query language. OWLAPI does not support it. You could use it for your tasks, but they look more OWL oriented than RDF oriented to me. Jena is a Java library supporting RDF, OWL, SPARQL and interfaces with reasoners such as Pellet. Depending on how you decide to solve the above tasks, it might fit more of your requirements than the OWLAPI.
Jena tutorials:
https://jena.apache.org/tutorials/index.html
OWLAPI documentation:
https://github.com/owlcs/owlapi/wiki/Documentation
I have been interested in formal methods for some time. I have used formal methods to reason about some very specific sub-areas of a few projects I have been working on. I was never able to convince other team members to try the same let alone specify an entire domain with a formal method.
One method I have found particularly interesting is Alloy. I think that it may "scale" better as foundation for an entire project because it is conceptually and notationally very close to actual programming languages. Furthermore, the tools are quite solid so that the benefits of model verification are readily available.
I'd be very much interested to hear about any real-world experiences you folks might have had with using Alloy in your projects. Do you feel that it has helped you in designing a better domain model? Did find errors in your domain model during verification? Would you use it again?
I've used Alloy on a few projects and have found it helpful; on some but not all of those projects I have been able to persuade others involved to use Alloy as well, or at least to work with the Alloy models I wrote. These projects may or may not be what you have in mind in asking for 'real-world' projects, but they certainly took place in the part of the real world I work in.
In 2006 and 2007 I created a partial Alloy model for the then-current draft of the W3C XProc specification; as far as I could tell, most members of the working group never read the paper I wrote (at http://www.w3.org/XML/XProc/2006/12/alloy-models/models.html); they said "Oh, we changed that part of the spec last week, so what the model says is no longer relevant". But the paper did manage to persuade the editor of the spec that the abstract 'component' level described in the first draft of the spec was woefully underspecified and needed to be either fully specified or dropped. He dropped it, with (I think) good results for the readability and usability of the spec.
In 2010 I made an Alloy model of the XPath 1.0 data model, which uncovered some glitches in the specification. The reaction of most interested parties (including the W3C working group responsible for maintaining the XPath 1.0 spec) has, unfortunately, not been encouraging.
A research project I'm involved with has used Alloy to model the MLCD Overlap Corpus, a collection of sample documents and related information we are creating (hyperlinks suppressed at SO's insistence); the Alloy model found a couple of errors in our initial design for the corpus catalog, so it was well worth the effort.
And we have also used Alloy to formalize some modeling work we have done on the nature of transcription and on the extension of the type/token distinction to document structure (for our paper, look for the 2010 proceedings of Balisage: The Markup Conference). This lies a little bit outside Alloy's usual area of application, as it has nothing to do with software design, but Alloy's ability to check models for consistency and generate instances has been invaluable in showing us some of the logical consequences of this or that possible axiom for our model.
To answer your specific questions: yes, Alloy has helped me specify cleaner domain models, and yes, it has found errors and glitches. They have often been small, for the reasons Daniel Jackson explains in his book Software Abstractions: first, if you use models during design, you catch errors early, when everything is still small. And, second (in Jackson's words), "In hindsight, most software design issues are trivial."
He continues: "But if you don't address them head-on, trivial issues have a nasty habit of becoming nontrivial." My experience amply confirms this. Much better to head off such problems early. So yes, I will use Alloy again.
Yes, I've used Alloy and it's cousins industrially. Alloy has been most helpful in convincing me that my models weren't wildly wrong---or rather, showing me where they were wrong and gave rise to silly results. Other more specific tools, like Song's Athena and Guttman and Ramsdell's CPSA have been more useful in their narrower domains. What more would you like to hear about?
Belatedly adding to this thread... Eunsuk Kang has recently applied Alloy to perform security analyses of web APIs for some start ups (following many applications of Alloy in security such as Apurva's analysis of OAuth and Barth et al's analysis of browser based security mechanisms for CSRF etc); Pamela Zave has been working on an impressive analysis of Chord, a peer to peer storage system, and has recently written up a fix to the original algorithm.
Core principles and tenets for designing a system. is this really web 3.0?
The core principles would include understanding of RDF, RDFS, OWL and
how arbitrary knowledge can be represented using these specs.
Understanding of what reasoners can do with semantic data is essential.
Then comes the idea of intelligent agents.
Then comes understanding of why this is all needed and why it was designed that way.
This would give you the clue about how promising (or not) is this technology.
For the software architect it would be good to know how OWL data can be efficiently stored(in RDBMS or in any other way for example).
As for myself I find this interesting but in reality it is yet very far from the
point where average users can benefit from it on the regular Web.
I am currently trying to draw a set of UML diagrams to represent products, offers, orders, deliveries and payments. These diagrams have probably been invented by a million developers before me.
Are there any efforts to standardize the modeling of such common things? Or even the modeling of specific domains (for example car-manufacturing).
Do you know if there is some sort of repository containing UML diagrams (class diagrams, sequence diagrams, state diagrams...)?
There is a movement for documenting (as opposed to standardizing) models for certain domains. These are called analysis patterns and is a term Martin Fowler came up with. He actually wrote a book called Analysis patterns. Also, he has a dedicated section on his website where he presents some of these patterns accompanied by UML diagrams.
Maybe you'll find some inspiration that will help you in modeling your domain. I've stressed the word inspiration as I think different businesses have different requirements although they operate the same domain so the solutions you might read about may not be appropriate for your problem.
There are many tools out there that do both - but they're generally not free!
Microsoft Visio does both and is extensible. For UML artefacts they come with auto generators into VB/Java template code - but you can modify them to auto-generate any code. There are many users of Visio that have created models from which to use as templates.
Artisan Enterprize is by far the most powerful UML tool (but it's not cheap).
Some would argue that Rational Rose or RUP is the better tool
But for Car-Manufacturing and other similar real world modelling, by far the best tool is Mathworks Simulink (not because it's one of the most expensive). It is by far the best tool beccause you can animate the model - you can prove the model working before generating the slik code (in whatever grammar/language/other Models you care to push it)!
You can obtain a student license for around £180; with the 'real thing' pushing £4000 (for car-related artefacts). The full product with all the trimmings is about £15k. Simulink is also extensible with a C like language though there is a .Net addin and APIs to use a plethora of other langhuages. And, just like Visio there is a world-wide forum creating saleable, shareware & freeware real world model templates. Many world-wide Auto-Manufacturers are already using Simulink.
I think that MiniQuark question is really good and will sooner or later be provided by vendors such as Omondo, Rational IBM etc... Users doesn't just need tools, they need models out of the box and just add their business rules inside an existing well defined architecture. Why to develop from scratch a new architecture if the job has already be done ? In Java we use plenty of frameworks, existing methods etc...so why not to go one level higher and reuse architecture ? It is today impossible to guess how a project will evole and new demands are coming every day. We therefore need a stable architecture which has been tested previously and is extensible. I have seen so many projects starting with a nice architecture then realizing in the middle of the project that this is not what is the best and then changing their architecture. Renaming classes, splitting classes, creating packages etc...after the first iteration it is getting a real mess. Could you imagine what we found after 10 iterations !! a total mess !!
This mess would had been avoided if using a predefined model which has been tested previously because the missing class, or package etc..would have already been created and only a class rename would be sufficient for architecture purposes. Adding business rules methods will end the codding stage before deployment test.
I think there is a confusion between patterns and the initial question which is related to UML model re usability.
There is no today any reusable model out of the box which has been developped. This is really strange but the job has never been done or never been shared.
Omondo has tried to launch an initiative without real success. I have heard that they are working on hundred of out of box models which will be open source and given for free to the community. I hope this will be done because this is really important for me and would save me a lot of time at the beginning of a project.